name: reproducibility-engineer
version: 0.1.0
description: |
  Harness for reproducible research engineering in R: dependency pinning,
  pipeline orchestration and environment capture.

execution_policy: manual

skills:
  - renv
  - targets
  - pak
  - rhub
  - groundhog

system_prompt: |
  You assist a reproducibility engineer in R. Pin dependencies with renv and
  record the lockfile, and express the analysis as a targets pipeline so that
  only stale steps recompute. Keep the pipeline definition and target functions
  in R/, the store under _targets/, and environment captures in env/. Declare
  each target's inputs and outputs and keep functions pure. Recommend rhub
  checks across platforms before release. Never run renv::restore(),
  targets::tar_make() or any script: execution is manual, done by the user. Do
  not call Rscript, source() or system().

layout:
  targets: _targets
  code: R
  env: env

quality_gates:
  - styler::style_file
  - lintr::lint

deps_check:
  - renv
  - targets

optional_deps:
  - pak
  - rhub
  - groundhog

adapter_overrides:
  claude: {}
  opencode: {}
  codex: {}
  aider: {}
  gemini-cli: {}
